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fix: disable adding prefix 'M_' and 'R_' in exprotModel function #356

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merged 2 commits into from
Aug 12, 2021
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fix: disable adding prefix 'M_' and 'R_' in exprotModel function #356

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202087d
fix: remove prefix 'M_' and 'R_' in exprotModel function
haowang-bioinfo Jul 15, 2021
1c0e32f
fix: remove prefix `c_` and remaining `R_`
haowang-bioinfo Aug 12, 2021
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12 changes: 6 additions & 6 deletions io/exportModel.m
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Original file line number Diff line number Diff line change
Expand Up @@ -281,13 +281,13 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
end

if isfield(modelSBML.species,'metaid')
modelSBML.species(i).metaid=['M_' model.mets{i}];
modelSBML.species(i).metaid=model.mets{i};
end
if isfield(modelSBML.species, 'name')
modelSBML.species(i).name=model.metNames{i};
end
if isfield(modelSBML.species, 'id')
modelSBML.species(i).id=['M_' model.mets{i}];
modelSBML.species(i).id=model.mets{i};
end
if isfield(modelSBML.species, 'compartment')
modelSBML.species(i).compartment=model.comps{model.metComps(i)};
Expand Down Expand Up @@ -329,7 +329,7 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
end
end
if ~isempty(model.metMiriams{i}) || hasInchi==true
modelSBML.species(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_M_' model.mets{i} '">'];
modelSBML.species(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.mets{i} '">'];
modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<bqbiol:is><rdf:Bag>'];
if ~isempty(model.metMiriams{i})
modelSBML.species(i).annotation=[modelSBML.species(i).annotation getMiriam(model.metMiriams{i})];
Expand Down Expand Up @@ -475,7 +475,7 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
end

if isfield(modelSBML.reaction,'metaid')
modelSBML.reaction(i).metaid=['R_' model.rxns{i}];
modelSBML.reaction(i).metaid=model.rxns{i};
end

%Export notes information
Expand Down Expand Up @@ -522,7 +522,7 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
modelSBML.reaction(i).name=model.rxnNames{i};
end
if isfield(modelSBML.reaction, 'id')
modelSBML.reaction(i).id=['R_' model.rxns{i}];
modelSBML.reaction(i).id=model.rxns{i};
end

%Add the information about reactants and products
Expand Down Expand Up @@ -574,7 +574,7 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
modelSBML.groups_group.sboTerm = 633;
tmpStruct=modelSBML.groups_group;

rxns=strcat('R_',model.rxns);
rxns=model.rxns;
if ~any(cellfun(@iscell,model.subSystems))
if ~any(~cellfun(@isempty,model.subSystems))
subSystems = {};
Expand Down